3C1V - JenaLib

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Title :   THE 1.5 A CRYSTAL STRUCTURE OF CA2+-BOUND S100A4

Authors :   A. R. Gingras, I. L. Barsukov

Date :   24 Jan 08 (Deposition) - 01 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   S100A4, Ca2+-Bound, Calcium-Bound, Calcium Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. R. Gingras, J. Basran, A. Prescott, M. Kriajevska, C. R. Bagshaw, I. L. Barsukov
Crystal Structure Of The Ca(2+)-Form And Ca(2+)-Binding Kinetics Of Metastasis-Associated Protein, S100A4
Febs Lett. V. 582 1651 2008
PubMed-ID: 18435928 | Reference-DOI: 10.1016/J.FEBSLET.2008.04.017
(for further references see the PDB file header)

Molecule 1 - PROTEIN S100-A4
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	BL21(DE3)
	Expression System Vector Type	:	PLASMID
	Gene	:	S100A4
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Synonym	:	S100 CALCIUM-BINDING PROTEIN A4, METASTASIN, PROTEIN MTS1, PLACENTAL CALCIUM-BINDING PROTEIN, CALVASCULIN

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	CA	8	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP D:63 , ASN D:65 , ASP D:67 , GLU D:69 , GLU D:74	BINDING SITE FOR RESIDUE CA D 102
2	AC2	SOFTWARE	SER D:20 , GLU D:23 , ASP D:25 , LYS D:28 , GLU D:33	BINDING SITE FOR RESIDUE CA D 103
3	AC3	SOFTWARE	SER B:20 , GLU B:23 , ASP B:25 , LYS B:28 , GLU B:33	BINDING SITE FOR RESIDUE CA B 102
4	AC4	SOFTWARE	ASP B:63 , ASN B:65 , ASP B:67 , GLU B:69 , GLU B:74	BINDING SITE FOR RESIDUE CA B 103
5	AC5	SOFTWARE	SER C:20 , GLU C:23 , ASP C:25 , LYS C:28 , GLU C:33	BINDING SITE FOR RESIDUE CA C 102
6	AC6	SOFTWARE	ASP C:63 , ASN C:65 , ASP C:67 , GLU C:69 , GLU C:74	BINDING SITE FOR RESIDUE CA C 103
7	AC7	SOFTWARE	SER A:20 , GLU A:23 , ASP A:25 , LYS A:28 , GLU A:33	BINDING SITE FOR RESIDUE CA A 102
8	AC8	SOFTWARE	ASP A:63 , ASN A:65 , ASP A:67 , GLU A:69 , GLU A:74	BINDING SITE FOR RESIDUE CA A 103

(no "SS Bond" information available for 3C1V)

Asymmetric Unit

No.	Residues
1	Gln B:97	-	Pro B:98
2	Gln D:97	-	Pro D:98

(no "SAP(SNP)/Variant" information available for 3C1V)

Asymmetric Unit (3, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	S10A4_HUMAN	50-85	4	A:50-85 B:50-85 C:50-85 D:50-85
2	S100_CABP	PS00303	S-100/ICaBP type calcium binding protein signature.	S10A4_HUMAN	58-79	4	A:58-79 B:58-79 C:58-79 D:58-79
3	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	S10A4_HUMAN	63-75	4	A:63-75 B:63-75 C:63-75 D:63-75

Biological Unit 1 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	S10A4_HUMAN	50-85	2	A:50-85 B:50-85 - -
2	S100_CABP	PS00303	S-100/ICaBP type calcium binding protein signature.	S10A4_HUMAN	58-79	2	A:58-79 B:58-79 - -
3	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	S10A4_HUMAN	63-75	2	A:63-75 B:63-75 - -

Biological Unit 2 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	S10A4_HUMAN	50-85	2	- - C:50-85 D:50-85
2	S100_CABP	PS00303	S-100/ICaBP type calcium binding protein signature.	S10A4_HUMAN	58-79	2	- - C:58-79 D:58-79
3	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	S10A4_HUMAN	63-75	2	- - C:63-75 D:63-75

Asymmetric Unit (2, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000368716	2a	ENSE00001928713	chr1:153518361-153518229	133	S10A4_HUMAN	-	0	0	-	-
1.4c	ENST00000368716	4c	ENSE00002173615	chr1:153517285-153517130	156	S10A4_HUMAN	1-47	47	4	A:2-47 B:2-47 C:2-47 D:2-47	46 46 46 46
1.5c	ENST00000368716	5c	ENSE00001447832	chr1:153516399-153516089	311	S10A4_HUMAN	48-101	54	4	A:48-94 B:48-98 C:48-94 D:48-98	47 51 47 51

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:93
 aligned with S10A4_HUMAN | P26447 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:93
                                    11        21        31        41        51        61        71        81        91   
           S10A4_HUMAN    2 ACPLEKALDVMVSTFHKYSGKEGDKFKLNKSELKELLTRELPSFLGKRTDEAAFQKLMSNLDSNRDNEVDFQEYCVFLSCIAMMCNEFFEGFP 94
               SCOP domains d3c1va_ A: automated matches                                                                  SCOP domains
               CATH domains 3c1vA00 A:2-94 EF-hand                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------EF_HAND_2  PDB: A:50-85             --------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------S100_CABP  PDB: A:58-7--------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------EF_HAND_1    ------------------- PROSITE (3)
               Transcript 1 Exon 1.4c  PDB: A:2-47 UniProt: 1-47          Exon 1.5c  PDB: A:48-94 UniProt: 48-101         Transcript 1
                  3c1v A  2 ACPLEKALDVMVSTFHKYSGKEGDKFKLNKSELKELLTRELPSFLGKRTDEAAFQKLMSNLDSNRDNEVDFQEYCVFLSCIAMMCNEFFEGFP 94
                                    11        21        31        41        51        61        71        81        91

Chain B from PDB  Type:PROTEIN  Length:97
 aligned with S10A4_HUMAN | P26447 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:97
                                    11        21        31        41        51        61        71        81        91       
           S10A4_HUMAN    2 ACPLEKALDVMVSTFHKYSGKEGDKFKLNKSELKELLTRELPSFLGKRTDEAAFQKLMSNLDSNRDNEVDFQEYCVFLSCIAMMCNEFFEGFPDKQP 98
               SCOP domains d3c1vb_ B: automated matches                                                                      SCOP domains
               CATH domains 3c1vB00 B:2-98 EF-hand                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------EF_HAND_2  PDB: B:50-85             ------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------S100_CABP  PDB: B:58-7------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------EF_HAND_1    ----------------------- PROSITE (3)
               Transcript 1 Exon 1.4c  PDB: B:2-47 UniProt: 1-47          Exon 1.5c  PDB: B:48-98 UniProt: 48-101             Transcript 1
                  3c1v B  2 ACPLEKALDVMVSTFHKYSGKEGDKFKLNKSELKELLTRELPSFLGKRTDEAAFQKLMSNLDSNRDNEVDFQEYCVFLSCIAMMCNEFFEGFPDKQP 98
                                    11        21        31        41        51        61        71        81        91

Chain C from PDB  Type:PROTEIN  Length:93
 aligned with S10A4_HUMAN | P26447 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:93
                                    11        21        31        41        51        61        71        81        91   
           S10A4_HUMAN    2 ACPLEKALDVMVSTFHKYSGKEGDKFKLNKSELKELLTRELPSFLGKRTDEAAFQKLMSNLDSNRDNEVDFQEYCVFLSCIAMMCNEFFEGFP 94
               SCOP domains d3c1vc_ C: automated matches                                                                  SCOP domains
               CATH domains 3c1vC00 C:2-94 EF-hand                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------EF_HAND_2  PDB: C:50-85             --------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------S100_CABP  PDB: C:58-7--------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------EF_HAND_1    ------------------- PROSITE (3)
               Transcript 1 Exon 1.4c  PDB: C:2-47 UniProt: 1-47          Exon 1.5c  PDB: C:48-94 UniProt: 48-101         Transcript 1
                  3c1v C  2 ACPLEKALDVMVSTFHKYSGKEGDKFKLNKSELKELLTRELPSFLGKRTDEAAFQKLMSNLDSNRDNEVDFQEYCVFLSCIAMMCNEFFEGFP 94
                                    11        21        31        41        51        61        71        81        91

Chain D from PDB  Type:PROTEIN  Length:97
 aligned with S10A4_HUMAN | P26447 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:97
                                    11        21        31        41        51        61        71        81        91       
           S10A4_HUMAN    2 ACPLEKALDVMVSTFHKYSGKEGDKFKLNKSELKELLTRELPSFLGKRTDEAAFQKLMSNLDSNRDNEVDFQEYCVFLSCIAMMCNEFFEGFPDKQP 98
               SCOP domains d3c1vd_ D: automated matches                                                                      SCOP domains
               CATH domains 3c1vD00 D:2-98 EF-hand                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------EF_HAND_2  PDB: D:50-85             ------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------S100_CABP  PDB: D:58-7------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------EF_HAND_1    ----------------------- PROSITE (3)
               Transcript 1 Exon 1.4c  PDB: D:2-47 UniProt: 1-47          Exon 1.5c  PDB: D:48-98 UniProt: 48-101             Transcript 1
                  3c1v D  2 ACPLEKALDVMVSTFHKYSGKEGDKFKLNKSELKELLTRELPSFLGKRTDEAAFQKLMSNLDSNRDNEVDFQEYCVFLSCIAMMCNEFFEGFPDKQP 98
                                    11        21        31        41        51        61        71        81        91

Legend:		→ Mismatch	(orange background)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: EF-hand (657)

Family: S100 proteins (101)

Protein domain: automated matches (32)

Human (Homo sapiens) [TaxId: 9606] (30)

1a	d3c1va_	A:
1b	d3c1vb_	B:
1c	d3c1vc_	C:
1d	d3c1vd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: EF-hand (412)

Human (Homo sapiens) (106)

1a	3c1vA00	A:2-94
1b	3c1vC00	C:2-94
1c	3c1vB00	B:2-98
1d	3c1vD00	D:2-98

(no "Pfam Domain" information available for 3C1V)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (S10A4_HUMAN | P26447)

molecular function
	GO:0050786	RAGE receptor binding	Interacting selectively and non-covalently with the RAGE receptor, the receptor for advanced glycation end-products.
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0048306	calcium-dependent protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in the presence of calcium.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0001837	epithelial to mesenchymal transition	A transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
	GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB signaling	Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0043005	neuron projection	A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

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	3c1v
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	S10A4_HUMAN \| P26447	:	1m31 2lnk 2mrd 2q91 3cga 3ko0 3m0w 3zwh 4cfq 4cfr 4eto 4hsz 5lpu

(no "Related Entries Specified in the PDB File" available for 3C1V)

Description

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Ligands, Modified Residues, Ions (1, 8)

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SS Bonds (0, 0)

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